Impact of Tandem Repeats on the Scaling of Nucleotide Sequences

Techniques such as detrended fluctuation analysis (DFA) and its extensions have been widely used to determine the nature of scaling in nucleotide sequences. In this brief communication we show that tandem repeats which are ubiquitous in nucleotide sequences can prevent reliable estimation of possible long-range correlations. Therefore, it is important to investigate the presence of tandem repeats prior to scaling exponent estimation.Comment: 14 Pages, 3 Figure

Citizen Sensor Data Mining, Social Media Analytics and Development Centric Web Applications

With the rapid rise in the popularity of social media (500M+ Facebook users, 100M+ twitter users), and near ubiquitous mobile access (4.1 billion actively-used mobile phones), the sharing of observations and opinions has become common-place (nearly 100M tweets a day, 1.8 trillion SMSs in US last year). This has given us an unprecedented access to the pulse of a populace and the ability to perform analytics on social data to support a variety of socially intelligent applications -- be it towards targeted online content delivery, crisis management, organizing revolutions or promoting social development in underdeveloped and developing countries. This tutorial will address challenges and techniques for building applications that support a broad variety of users and types of social media. This tutorial will focus on social intelligence applications for social development, and cover the following research efforts in sufficient depth: 1) understanding and analysis of informal text, esp. microblogs (e.g., issues of cultural entity extraction and role of semantic/background knowledge enhanced techniques), and 2) building social media analytics platforms. Technical insights will be coupled with identification of computational techniques and real-world examples

Qualitative Assessment of Gene Expression in Affymetrix Genechip Arrays

Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array and in turn govern the gene expression. In the present study, we make several interesting observations. We show that there is considerable correlation between the probe intensities across the array which defy the independence assumption. While the mechanism behind such correlations is unclear, we show that scaling behavior and the profiles of perfect match (PM) as well as mismatch (MM) probes are similar and immune to background subtraction. We believe that the observed correlations are possibly an outcome of inherent non-stationarities or patchiness in the array devoid of biological significance. This is demonstrated by inspecting their scaling behavior and profiles of the PM and MM probe intensities obtained from publicly available Genechip arrays from three eukaryotic genomes, namely: Drosophila Melanogaster, Homo Sapiens and Mus musculus across distinct biological paradigms and across laboratories, with and without background subtraction. The fluctuation functions were estimated using detrended fluctuation analysis (DFA) with fourth order polynomial detrending. The results presented in this study provide new insights into correlation signatures of PM and MM probe intensities and suggests the choice of DFA as a tool for qualitative assessment of Affymetrix Genechip microarrays prior to their analysis. A more detailed investigation is necessary in order to understand the source of these correlations.Comment: 22 Pages, 7 Figures, 1 Tabl

Artist Ranking Through Analysis of On-line Community Comments

We describe an approach to measure the popularity of music tracks, albums and artists by analyzing the comments of music listeners in social networking online communities such as MySpace. This measure of popularity appears to be more accurate than the traditional measure based on album sales figures, as demonstrated by our focus group study. We faced many challenges in our attempt to generate a popularity ranking from the user comments on social networking sites, e.g., broken English sentences, comment spam, etc. We discuss the steps we took to overcome these challenges and describe an end to end system for generating a new popularity measure based on online comments, and the experiments performed to evaluate its success

Monetizing User Activity on Social Networks - Challenges and Experiences

Abstract—This work summarizes challenges and experiences in monetizing user activity on public forums on social network sites. We present a approach that identifies the monetization potential of user posts and eliminates off-topic content to identify the most relevant and monetizable keywords for advertising. Preliminary studies using data from MySpace and Facebook show that 52 % of ad impressions generated using keywords from our system were more targeted compared to the 30 % relevant impressions generated without using our system. Keywords- user activity, off-topic noise, contentextual ads I

3D tumor tissue analogs and their orthotopic implants for understanding tumor-targeting of microenvironment-responsive nanosized chemotherapy and radiation

AbstractAn appropriate representation of the tumor microenvironment in tumor models can have a pronounced impact on directing combinatorial treatment strategies and cancer nanotherapeutics. The present study develops a novel 3D co-culture spheroid model (3D TNBC) incorporating tumor cells, endothelial cells and fibroblasts as color-coded murine tumor tissue analogs (TTA) to better represent the tumor milieu of triple negative breast cancer in vitro. Implantation of TTA orthotopically in nude mice, resulted in enhanced growth and aggressive metastasis to ectopic sites. Subsequently, the utility of the model is demonstrated for preferential targeting of irradiated tumor endothelial cells via radiation-induced stromal enrichment of galectin-1 using anginex conjugated nanoparticles (nanobins) carrying arsenic trioxide and cisplatin. Demonstration of a multimodal nanotherapeutic system and inclusion of the biological response to radiation using an in vitro/in vivo tumor model incorporating characteristics of tumor microenvironment presents an advance in preclinical evaluation of existing and novel cancer nanotherapies.From the Clinical EditorExisting in-vivo tumor models are established by implanting tumor cells into nude mice. Here, the authors described their approach 3D spheres containing tumor cells, enodothelial cells and fibroblasts. This would mimic tumor micro-environment more realistically. This interesting 3D model should reflect more accurately tumor response to various drugs and would enable the design of new treatment modalities

Spatio-Temporal-Thematic Analysis of Citizen Sensor Data: Challenges and Experiences

We present work in the spatio-temporal-thematic analysis of citizen-sensor observations pertaining to real-world events. Using Twitter as a platform for obtaining crowd-sourced observations, we explore the interplay between these 3 dimensions in extracting insightful summaries of social perceptions behind events. We present our experiences in building a web mashup application, Twitris that extracts and facilitates the spatio-temporal-thematic exploration of event descriptor summaries

Multifunctional Clay in Pharmaceuticals

Clay has its widespread applications in pharmaceuticals from ancient world to modern era. It is one of the excellent excipients present in the commercially available pharmaceuticals. Its use in many of dosage forms viz. in suspension, emulsion, ointments, gels, tablet and as drug delivery carrier as suspending agent, emulsifying agent, stiffening agent, binder, diluent, opacifier, and as release retardant have been explored in many studies. Variety of minerals is used as both excipient and as an active ingredient; among that kaolinite, talc, and gypsum are important. Their inertness, low toxicity, versatile physiochemical properties and cost effectiveness has increased its usage in pharma industries. Many minerals have its own pharmacological action as antacid, anti-bacterial, anti-emetic, anti- diarrheal agent and as skin protectant etc. Their unique structure which helps them to absorb material onto their layered sheets has opened a wide variety of applications in drug delivery. The understanding of surface chemistry and particle size distribution of clay minerals has led the pharmaceutical field in many directions and future perspectives